The thing about goofballs and screw-ups on the Joe team in the cartoon...if everyone were a 100% competent, serious professional the show would be boring, the characters mostly flat. (And the show wasn't about the real armed forces anymore than C.O.P.S. was about actual law enforcement.)

Same with Cobra. People sometimes diss the Dreadnoks. They aren't Cobra's ideal, they are Zartan's entourage...Cobra wants Zartan's services, and he and the Dreads are a package deal. Even the cartoon writer's guide says if Cobra took over, the Dreadnoks would the type of people Cobra would line up against a wall and have shot. The comic made less sense that the Dreadnoks were kept around when Zartan abandoned Cobra, part of that was Zarana's pull...but her level of competence was spotty.

In the comics, once GI JOE knew the Terrordrome secret, that Cobra plot was foiled (or logically should've been). After that they seemed to push arm sales...Cobra Commander was just a more psychotic Destro. He came back from the dead and there was a sense, oh, now he's really gonna take on the world. But his brainwashing of Millville was just to have more factory workers to make weapons. Destro meanwhile had given up evil. Things just didn't work. Especially Firefly acting like a Cobra Commander wannabe.

The series really ended with the Snake-Eyes trilogy. Think about it. Original Cobra Commander was still "dead". Destro and the Baroness turned over a new leaf. Zartan had or was on the cusp of doing so. Cobra's most powerful players were out of the game. The next fifty or so issues were Cobra commander acting like a twit and Snake-Eyes just NOT killing him (even though it was clearly within his power a few times), Transformers, a castle that changes shape and hands every few issues.